@article{2345, abstract = {We give upper bounds for the number of spin-1/2 particles that can be bound to a nucleus of charge Z in the presence of a magnetic field B, including the spin-field coupling. We use Lieb's strategy, which is known to yield Nc < 2Z + 1 for magnetic fields that go to zero at infinity, ignoring the spin-field interaction. For particles with fermionic statistics in a homogeneous magnetic field our upper bound has an additional term of the order of Z × min {(B/Z3)2/5, 1 + | 1n(B/Z3)|2}.}, author = {Seiringer, Robert}, issn = {0305-4470}, journal = {Journal of Physics A: Mathematical and General}, number = {9}, pages = {1943 -- 1948}, publisher = {IOP Publishing Ltd.}, title = {{On the maximal ionization of atoms in strong magnetic fields}}, doi = {10.1088/0305-4470/34/9/311}, volume = {34}, year = {2001}, } @article{2341, abstract = {We study the ground state properties of an atom with nuclear charge Z and N bosonic "electrons" in the presence of a homogeneous magnetic field B. We investigate the mean field limit N→∞ with N / Z fixed, and identify three different asymptotic regions, according to B≪Z2,B∼Z2,andB≫Z2 . In Region 1 standard Hartree theory is applicable. Region 3 is described by a one-dimensional functional, which is identical to the so-called Hyper-Strong functional introduced by Lieb, Solovej and Yngvason for atoms with fermionic electrons in the region B≫Z3 ; i.e., for very strong magnetic fields the ground state properties of atoms are independent of statistics. For Region 2 we introduce a general magnetic Hartree functional, which is studied in detail. It is shown that in the special case of an atom it can be restricted to the subspace of zero angular momentum parallel to the magnetic field, which simplifies the theory considerably. The functional reproduces the energy and the one-particle reduced density matrix for the full N-particle ground state to leading order in N, and it implies the description of the other regions as limiting cases.}, author = {Baumgartner, Bernhard and Seiringer, Robert}, issn = {1424-0637}, journal = {Annales Henri Poincare}, number = {1}, pages = {41 -- 76}, publisher = {Birkhäuser}, title = {{Atoms with bosonic "electrons" in strong magnetic fields}}, doi = {10.1007/PL00001032}, volume = {2}, year = {2001}, } @article{2346, abstract = {By means of a generalization of the Fefferman - de la Llave decomposition we derive a general lower bound on the interaction energy of one-dimensional quantum systems. We apply this result to a specific class of lowest Landau band wave functions.}, author = {Hainzl, Christian and Seiringer, Robert}, issn = {0377-9017}, journal = {Letters in Mathematical Physics}, number = {2}, pages = {133 -- 142}, publisher = {Springer}, title = {{Bounds on one-dimensional exchange energies with application to lowest Landau band quantum mechanics}}, doi = {10.1023/A:1010951905548}, volume = {55}, year = {2001}, } @inproceedings{2340, abstract = {Recent experimental breakthroughs in the treatment of dilute Bose gases have renewed interest in their quantum mechanical description, respectively in approximations to it. The ground state properties of dilute Bose gases confined in external potentials and interacting via repulsive short range forces are usually described by means of the Gross-Pitaevskii energy functional. In joint work with Elliott H. Lieb and Jakob Yngvason its status as an approximation for the quantum mechanical many-body ground state problem has recently been rigorously clarified. We present a summary of this work, for both the two-and three-dimensional case. }, author = {Seiringer, Robert}, editor = {Demuth, Michael and Schultze, Bert}, isbn = {9783034894838}, location = {Clausthal, Germany}, pages = {307 -- 314}, publisher = {Birkhäuser}, title = {{Bosons in a trap: Asymptotic exactness of the Gross-Pitaevskii ground state energy formula}}, doi = {10.1007/978-3-0348-8231-6}, volume = {126}, year = {2001}, } @article{1452, abstract = {In this Note we present pairs of hyperkähler orbifolds which satisfy two different versions of mirror symmetry. On the one hand, we show that their Hodge numbers (or more precisely, stringy E-polynomials) are equal. On the other hand, we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a Calabi-Yau and its mirror should fiber over the same real manifold, with special Lagrangian fibers which are tori dual to each other. Our examples arise as moduli spaces of local systems on a curve with structure group SL(n); the mirror is the corresponding space with structure group PGL(n). The special Lagrangian tori come from an algebraically completely integrable Hamiltonian system: the Hitchin system.}, author = {Hausel, Tamas and Thaddeus, Michael}, issn = {0764-4442}, journal = {Comptes Rendus de l'Academie des Sciences - Series I: Mathematics}, number = {4}, pages = {313 -- 318}, publisher = {Elsevier}, title = {{Examples of mirror partners arising from integrable systems}}, doi = {10.1016/S0764-4442(01)02057-2}, volume = {333}, year = {2001}, } @article{888, abstract = {BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.}, author = {Jordan, Ingo and Kondrashov, Fyodor and Rogozin, Igor and Tatusov, Roman and Wolf, Yuri and Koonin, Eugene}, issn = {1465-6906}, journal = {Genome Biology}, number = {12}, publisher = {BioMed Central}, title = {{Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins }}, doi = {10.1186/gb-2001-2-12-research0053}, volume = {2}, year = {2001}, } @article{1453, abstract = {In this Letter we exhibit a one-parameter family of new Taub-NUT instantons parameterized by a half-line. The endpoint of the half-line will be the reducible Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form, while at an inner point we recover the Pope-Yuille instanton constructed as a projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra. Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT space with a point singularity, rescale the metric and project the obtained Levi-Civitá connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess the full U(2) symmetry, and thus provide more solutions to the recently proposed U(2) symmetric ansatz of Kim and Yoon.}, author = {Etesi, Gábor and Hausel, Tamas}, issn = {0370-2693}, journal = {Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics}, number = {1-2}, pages = {189 -- 199}, publisher = {Elsevier}, title = {{Geometric construction of new Yang-Mills instantons over Taub-NUT space}}, doi = {10.1016/S0370-2693(01)00821-8}, volume = {514}, year = {2001}, } @article{1454, abstract = {We address the problem of finding Abelian instantons of finite energy on the Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic 2-forms on the space. Gibbons found a non-topological L2 harmonic form in the Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate his construction in the case of the Euclidean Schwarzschild manifold and find a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number 2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.}, author = {Etesi, Gábor and Hausel, Tamas}, issn = {0393-0440}, journal = {Journal of Geometry and Physics}, number = {1-2}, pages = {126 -- 136}, publisher = {Elsevier}, title = {{Geometric interpretation of Schwarzschild instantons}}, doi = {10.1016/S0393-0440(00)00040-1}, volume = {37}, year = {2001}, } @article{855, abstract = {Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5′ UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5′ UTR. Similarly, a negative correlation exists between the 'strength' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5′ UTRs with multiple upstream ATGs have a 'weak' start context, and in contrast, cDNAs containing short 5′ UTRs without ATGs have 'strong' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative splicing.}, author = {Rogozin, Igor and Kochetov, Alex and Kondrashov, Fyodor and Koonin, Eugene and Milanesi, Luciano}, issn = {1367-4803}, journal = {Bioinformatics}, number = {10}, pages = {890 -- 900}, publisher = {Oxford University Press}, title = {{Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon}}, doi = {10.1093/bioinformatics/17.10.890}, volume = {17}, year = {2001}, } @article{874, abstract = {Sex is thought to facilitate accumulation of initially rare beneficial mutations by allowing simultaneous allele replacements at many loci. However, this advantage of sex depends on a restrictive assumption that the fitness of a genotype is determined by fitness potential, a single intermediate variable to which all loci contribute additively, so that new alleles can accumulate in any order. Individual-based simulations of sexual and asexual populations reveal that under generic selection, sex often retards adaptive evolution. When new alleles are beneficial only if they accumulate in a prescribed order, a sexual population may evolve two or more times slower than an asexual population because only asexual reproduction allows some overlap of successive allele replacements. Many other fitness surfaces lead to an even greater disadvantage of sex. Thus, either sex exists in spite of its impact on the rate of adaptive allele replacements, or natural fitness surfaces have rather specific properties, at least at the scale of intrapopulation genetic variability.}, author = {Kondrashov, Fyodor and Kondrashov, Alexey}, issn = {0027-8424}, journal = {PNAS}, number = {21}, pages = {12089 -- 12092}, publisher = {National Academy of Sciences}, title = {{Multidimensional epistasis and the disadvantage of sex}}, doi = {10.1073/pnas.211214298}, volume = {98}, year = {2001}, } @article{867, abstract = {Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For ∼10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes.}, author = {Kondrashov, Fyodor and Koonin, Eugene}, issn = {0964-6906}, journal = {Human Molecular Genetics}, number = {23}, pages = {2661 -- 2669}, publisher = {Oxford University Press}, title = {{Origin of alternative splicing by tandem exon duplication}}, doi = {10.1093/hmg/10.23.2661}, volume = {10}, year = {2001}, } @article{851, abstract = {The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.}, author = {Rogozin, Igor and Kondrashov, Fyodor and Glazko, Galina}, issn = {1059-7794}, journal = {Human Mutation}, number = {2}, pages = {83 -- 102}, publisher = {Wiley-Blackwell}, title = {{Use of mutation spectra analysis software}}, doi = {10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E}, volume = {17}, year = {2001}, } @article{841, author = {Wolf, Yuri and Kondrashov, Fyodor and Koonin, Eugene}, issn = {0168-9479}, journal = {Trends in Genetics}, number = {9}, pages = {499 -- 501}, publisher = {Elsevier}, title = {{Footprints of primordial introns on the eukaryotic genome: still no clear traces }}, doi = {10.1016/S0168-9525(01)02376-9}, volume = {17}, year = {2001}, } @article{11755, abstract = {Hyperlink analysis algorithms significantly improve the relevance of the search results on the Web, so much so that all major Web search engines claim to use some type of hyperlink analysis. However, the search engines do not disclose details about the type of hyperlink analysis they perform, mostly to avoid manipulation of search results by Web-positioning companies. The article discusses how hyperlink analysis can be applied to ranking algorithms, and surveys other ways Web search engines can use this analysis.}, author = {Henzinger, Monika H}, issn = {1941-0131}, journal = {IEEE Internet Computing}, number = {1}, pages = {45--50}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Hyperlink analysis for the Web}}, doi = {10.1109/4236.895141}, volume = {5}, year = {2001}, }